A Stem Cell-Based Epigenetic Memory Mediates Interferon Response-Heterogeneity within the Hematopoietic System

Mature blood and immune cells show broad inter- and intra-cell type-specific heterogeneity with respect to metabolic activity, gene expression patterns, differentiation capacity and responsiveness to cytokines such as interferons (IFNs). This diversity is of crucial importance to maintain the capacity of the immune system to appropriately react to a wide range of pathogenic insults, thereby mediating protective immunity. However, it remains poorly understood how such heterogeneity is generated and maintained. Until now, intra-cell type heterogeneity observed in blood and immune effector cells has mainly been attributed to extrinsic factors, such as differences in niche localization or cytokine exposure via paracrine signaling. Here, we show that intra-cell type heterogeneity can be established already at the stem cell-level and stably inherited to mature blood and immune cells through a stem cell-based epigenetic memory.

Using distinct IFN reporter mouse models, we identified two subpopulations within the hematopoietic stem cell (HSC) compartment that strongly differ with regard to their IFN responsiveness (hereafter referred to as IFN-primed and IFN-non-primed HSCs). Serial transplantation of highly purified HSC subsets demonstrated that both IFN-primed and IFN-non-primed subpopulations are capable of driving long-term hematopoiesis. However, stem, progenitor and mature cells deriving from the two distinct HSC subsets stably inherited the IFN-priming status of their mother HSCs throughout serial rounds of transplantation. This suggested that IFN-priming heterogeneity observed in mature blood and immune cells is established at the stem cell level and inherited for thousands of cell generations.

To investigate the consequences of the inherited IFN-priming state, we challenged mice with a broad spectrum of inflammatory cytokines, immunostimulants and viruses and subjected subpopulations to bulk and single-cell transcriptional profiling. Strikingly, populations with high IFN-priming mounted acute type-I IFN responses much more efficiently if compared to populations with low IFN-priming, suggesting that not only homeostatic IFN-priming but also responsiveness to acute IFNs is clonally determined at the stem cell level.

Next, we investigated the signaling pathways regulating IFN-priming. For this purpose, we subjected HSCs of mice lacking key components of the IFN signaling and production pathways to molecular characterization. These analyses revealed that IFN-priming is driven by homeostatic, cell-intrinsic IFNAR/IFNGR-STAT1 and TNF-α signaling. To elucidate the molecular mechanism facilitating stable inheritance of IFN-priming, we performed extensive epigenetic profiling of IFN-primed and IFN-non-primed subpopulations. The results suggested that inheritance of IFN-priming is mediated by a novel epigenetic mechanism and associated with epigenetic pervasiveness versus silencing in IFN-primed and IFN-non-primed HSCs, respectively.

Together, our data reveal a novel epigenetic stem cell-based memory that dictates IFN response heterogeneity in mature blood and immune cells. This finding will likely have far-reaching implications for the understanding of biological processes involved in antiviral responses, cancer immunosurveillance as well as autoimmunity.